LAMMPS (20 Jun 2017)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (../comm.cpp:90)
  using 1 OpenMP thread(s) per MPI task
# Solvated 5-mer peptide, run for 8ps in NVT

units           real
atom_style      full

pair_style      lj/charmm/coul/long 8.0 10.0 10.0
bond_style      harmonic
angle_style     charmm
dihedral_style  charmm
improper_style  harmonic
kspace_style    pppm 0.0001

read_data       data.peptide
  orthogonal box = (36.8402 41.0137 29.7681) to (64.2116 68.3851 57.1395)
  1 by 1 by 1 MPI processor grid
  reading atoms ...
  2004 atoms
  reading velocities ...
  2004 velocities
  scanning bonds ...
  3 = max bonds/atom
  scanning angles ...
  6 = max angles/atom
  scanning dihedrals ...
  14 = max dihedrals/atom
  scanning impropers ...
  1 = max impropers/atom
  reading bonds ...
  1365 bonds
  reading angles ...
  786 angles
  reading dihedrals ...
  207 dihedrals
  reading impropers ...
  12 impropers
  4 = max # of 1-2 neighbors
  7 = max # of 1-3 neighbors
  14 = max # of 1-4 neighbors
  18 = max # of special neighbors

neighbor        2.0 bin
neigh_modify    delay 5

thermo          50
#dump            dump1 all atom 100 peptide.dump

timestep        8

run_style respa 3 2 8 bond 1 dihedral 2 pair 2 kspace 3
Respa levels:
  1 = bond angle
  2 = dihedral improper pair
  3 = kspace

fix             1 all nvt temp 250.0 250.0 100.0 tchain 1
fix             cor all filter/corotate m 1.0
  19 = # of size 2 clusters
  0 = # of size 3 clusters
  3 = # of size 4 clusters
  0 = # of size 5 clusters
  646 = # of frozen angles
run             1000
PPPM initialization ...
WARNING: Using 12-bit tables for long-range coulomb (../kspace.cpp:321)
  G vector (1/distance) = 0.268725
  grid = 15 15 15
  stencil order = 5
  estimated absolute RMS force accuracy = 0.0228209
  estimated relative force accuracy = 6.87243e-05
  using double precision FFTs
  3d grid and FFT values/proc = 10648 3375
Neighbor list info ...
  update every 1 steps, delay 5 steps, check yes
  max neighbors/atom: 2000, page size: 100000
  master list distance cutoff = 12
  ghost atom cutoff = 12
  binsize = 6, bins = 5 5 5
  1 neighbor lists, perpetual/occasional/extra = 1 0 0
  (1) pair lj/charmm/coul/long, perpetual
      attributes: half, newton on
      pair build: half/bin/newton
      stencil: half/bin/3d/newton
      bin: standard
Per MPI rank memory allocation (min/avg/max) = 22.72 | 22.72 | 22.72 Mbytes
Step Temp E_pair E_mol TotEng Press 
       0     190.0857   -6442.7438    70.391457   -5237.4338    20361.984 
      50    239.47667   -7205.1006    1092.7664   -4682.5237   -23733.122 
     100    244.63086   -6788.0793    422.97204   -4904.5234    16458.011 
     150    240.79042   -7267.0791    966.31411   -4863.1107   -13554.894 
     200    254.77122   -6868.5713    591.00071   -4756.4431    10532.563 
     250    241.87417   -7264.9349     856.9357   -4963.8743   -9043.4359 
     300    251.37775      -6976.8    650.55612   -4825.3773    6986.2021 
     350    250.81494   -7286.7011    880.11184   -4909.0829   -6392.4665 
     400    247.55673   -7104.4036    701.89555   -4924.4551    4720.7811 
     450    258.54988   -7215.3011    832.23692   -4839.3759   -3446.3859 
     500    246.80928   -7151.2468    715.61007   -4962.0464    2637.5769 
     550    246.20721   -7159.0464    805.24974   -4883.8011    -2725.227 
     600    250.62483   -7201.7688    806.10076   -4899.2968    770.22352 
     650    247.59777   -7260.1607    802.97277   -4978.8899   -430.42309 
     700    246.86951   -7286.2971    825.99865   -4986.3486   -427.88651 
     750    252.79268   -7307.8572     833.4822   -4965.0605   -614.74372 
     800    251.73191   -7315.2457    839.59859    -4972.666    952.56448 
     850    246.75844   -7303.6221    816.67112   -5013.6642   -2055.2823 
     900    251.00123   -7317.4219    825.12165   -4993.6817   -356.53166 
     950    259.20822   -7252.3466    854.62611   -4850.1016   -1719.5267 
    1000    245.72486   -7347.5547    811.48146   -5068.9576    -717.6136 
Loop time of 357.523 on 1 procs for 1000 steps with 2004 atoms

Performance: 1.933 ns/day, 12.414 hours/ns, 2.797 timesteps/s
32.0% CPU use with 1 MPI tasks x 1 OpenMP threads

MPI task timing breakdown:
Section |  min time  |  avg time  |  max time  |%varavg| %total
---------------------------------------------------------------
Pair    | 328.2      | 328.2      | 328.2      |   0.0 | 91.80
Bond    | 4.4815     | 4.4815     | 4.4815     |   0.0 |  1.25
Kspace  | 3.9448     | 3.9448     | 3.9448     |   0.0 |  1.10
Neigh   | 12.457     | 12.457     | 12.457     |   0.0 |  3.48
Comm    | 3.2147     | 3.2147     | 3.2147     |   0.0 |  0.90
Output  | 0.001689   | 0.001689   | 0.001689   |   0.0 |  0.00
Modify  | 3.937      | 3.937      | 3.937      |   0.0 |  1.10
Other   |            | 1.289      |            |       |  0.36

Nlocal:    2004 ave 2004 max 2004 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost:    11191 ave 11191 max 11191 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs:    708610 ave 708610 max 708610 min
Histogram: 1 0 0 0 0 0 0 0 0 0

Total # of neighbors = 708610
Ave neighs/atom = 353.598
Ave special neighs/atom = 2.34032
Neighbor list builds = 200
Dangerous builds = 200
unfix           cor
unfix           1




Please see the log.cite file for references relevant to this simulation

Total wall time: 0:05:57
